Interpretive Summary: Tan spot is a foliar disease of wheat caused by a fungal pathogen (Pyrenophora tritici-repentis). The fungus produces a host-selective toxin known as Ptr ToxA. Sensitivity to the toxin is controlled by a single gene in wheat designated Tsn1. The long-term objective of this work is to isolate the Tsn1 gene to gain knowledge regarding the molecular interaction between Tsn1 and Ptr ToxA so that novel strategies to obtain resistance can be devised. Through out evolution, members of the grass family such as wheat and rice have retained certain levels of conservation in genetic makeup and gene order (colinearity). This apparent conservation has led to the notion that information of the rice genome could be used to expedite gene discovery in wheat. Here, we describe the evaluation of macrocolinearity (chromosome level) and microcolinearity (DNA sequence level) between the chromosomal region encompassing the Tsn1 gene in wheat and the rice genome. Our results indicated that colinearity at both the macro and micro levels between the Tsn1 region and rice is not well conserved. While several instances of loose levels of colinearity were observed, frequent rearrangements and disruptions existed within the region under investigation. These results indicated that the Tsn1 region in wheat is highly rearranged compared to rice, and the rice genomic information will be of little use for isolating the Tsn1 gene.

Technical Abstract:
The Tsn1 gene in wheat confers sensitivity to a proteinaceous host-selective toxin (Ptr ToxA) produced by the tan spot fungus (Pyrenophora tritici-repentis) and lies within a gene-rich region of chromosome 5B. To determine the feasibility of using the rice genome sequence information for the map-based cloning of Tsn1, we evaluated colinearity between the wheat genomic region containing Tsn1 and the rice genome at the macro- and micro-levels. Evaluation of macrocolinearity was done by testing 28 expressed sequence markers (ESMs) spanning a 25.5 cM segment and encompassing Tsn1 for similarity to rice sequences. Twelve ESMs had no similarity to rice sequences, and 16 had similarity to sequences on seven different rice chromosomes. Segments of colinearity with rice chromosomes 3 and 9 were identified, but frequent rearrangements and disruptions occurred. Microcolinearity was evaluated by testing the sequences of 28 putative genes identified from BAC contigs of 205 and 548 kb flanking Tsn1 for similarity to rice genomic sequences. Fourteen of the predicted genes detected orthologous sequences on six different rice chromosomes, whereas the remaining 14 had no similarity with rice sequences. Four genes were colinear on rice chromosome 9, but multiple disruptions, rearrangements, and duplications were observed in wheat relative to rice. Our results agree with other studies indicating that wheat homoeologous group 5 chromosomes are highly rearranged relative to rice, and we conclude that rice is of little use as a vehicle for cloning Tsn1.